Drupal core allows for users to select their own comment settings, I don't think it should. Putting this as a bug because it's possibly the worst usability issue in core that there is.
1. There are eight possible options presented to the end-user (of the site, not just the administrator) if these settings are turned on, possibly twice on every page.
flat expanded oldest-first
flat expanded newest-first
flat collapsed oldest-first
flat collapsed newest-first
threaded expanded oldest-first
threaded expanded newest-first
threaded collapsed oldest-first
threaded collapsed newest-first
+ infinite variation when number of comments is taken into account
3. I think a lot of people would like comment settings per node type (so threaded for blogs, flat expanded for forums, that sort of thing) - allowing users to override this would get very complex.
4. I've never ever seen a drupal site using this.
> > users.sort
> > users.threshold
These are/were used by comment.module to store user preferences.
Probably can be dropped too, they are all 0 on d.o for all users.
This is an initial patch - removes the comment controls forms and theme functions, but leaves comment_get_display_setting and the db columns untouched. This is the kind of thing that could be done at the theme level by a contrib module, so those columns could be left in the database for one release cycle to provide an upgrade path. Also comment_get_display_setting would have to be refactored to take into account node types, which is probably another issue, and no patch for that today.
The one exception to this is maybe number of comments per page, I can see it being handy to set that and it can be done with very little cruft, but it should probably be a user account setting rather than a form on every page.
http://drupal.org/node/101013 is kind of related.